Just as Pee-Wee walks into the Joke Shop at the beginning of the film (after he chains his bike to the clown), there is a mini-poster of Elvira on the shop's wall. See more...
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Continuity: Early in the Warner Bros. studio chase sequence we see a team of security guards in pursuit of Pee-wee. Somehow the guard in front switches from using a golf cart to a bicycle, all within a few brief cuts. This is the same guard who pulled the right handle from Pee-wee's bike moments ago.
Revealing: After Pee-Wee tears through a Godzilla production in the Warner Bros. studios with his bike, he exits the stage, ending up on an alley where he turns left to evade the props and security guards on his tail - one of which has a motorbike. On the pavement beneath him is a curved skid mark from a previous take, not unlike the one left behind by the motorbike seconds later.
Continuity: In the pet store fire scene, you see an aquarium full of fish. At one point Pee Wee stops to rescue them by scooping them into a plastic bag filled with water. While he's doing this, the aquarium is nearly empty. In the last scene of the sequence (as he's running out of the store with the snakes), the aquarium is again chock-full of fish.
Continuity: In the scene where Andy chases Pee-wee down with a dinosaur bone, we can see Simone in the background flailing her arms and screaming Andy's name. At first she's walking towards a nearby staircase on the dinosaur's left side, but between cuts she quickly repositions and is now standing in front of the dinosaur's large foot instead.